ggraph网络图:指定节点坐标

Question

尝试使用ggraph包绘制网络并指定每个节点的坐标。虽然我可以用igraph包实现这一点，但我不能用ggraph包来实现这一点。

# reproducible example to generate a random graph
library(igraph)
g1 <- erdos.renyi.game(20, 1/2)
plot(g1)

# function to produce coordinates for each node in order of the node
# degree (number of links per node)
coord <- function(g){   
    n.nod <- length(V(g))
    mat.c <- matrix(0, nrow = n.nod, ncol = 2)
    deg <- degree(g)
    uniq.deg <- unique(deg)
    min.d <- min(deg); max.d<- max(deg)
    spa <- 10/(max.d - min.d) # how much to increment 0 to 10 space along y-axis

    divi.y.1 <- seq(from = min.d, to=max.d, by = 1)
    divi.y.2 <- seq(from = 0, to=10, by = spa)  # both have same length

    ind.x <- c(); ind.x[1] = 0
    for(x in 2:n.nod){
      ind.x[x] <- ind.x[x-1] + 0.1
      if(ind.x[x] >= 10){
        ind.x[x] = ind.x[x-1] - 0.1
      }  
    } 
 d1 <- data.frame(divi.y.1, divi.y.2)

 # plotting space of grid is (0,0), (0, 10), (10, 10), (10, 0)
 for(i in 1:n.nod){
    # y-axis in order
    inD <-  which(d1$divi.y.1 == deg[i])
    mat.c[i, 2] <- d1[inD,2]
 } 
 mat.c[, 1] <- ind.x
 return(data.frame(mat.c))
}

下面是绘制igraph对象的“老式”方法：

# plot igraph object - the old fashion way
x11()
plot(g1, layout = coord(g1), rescale = T, frame=T,
 vertex.frame.color = "black", edge.color = "lightsteelblue",
 edge.width = 1, vertex.label.cex = 1,
 vertex.label.color = "black", 
 main = "Nodes in order of degree: top have more links, bottom fewer links")

指向ggraph文档的链接是here。另请参阅用于ggraph的GitHub存储库，了解软件包安装说明(需要R.3.3以上版本)。下面是工作的ggraph图(但我没有指定每个节点的坐标)：

library(ggraph)
V(g1)$NaMe <- seq(1:20)

x11()
   ggraph(g1, 'igraph', algorithm = 'kk') +  
   geom_edge_link(colour = "black", alpha = 0.8, show.legend = F) + 
   geom_node_label(aes(label = NaMe)) + ggtitle("ggraph plot: How to allocate coordinate for each node?") + 
   ggforce::theme_no_axes()

下面是我使用每个节点的指定坐标绘制ggraph图的尝试。按照ggraph()中类似的示例和早期的尝试，将节点的坐标传递到绘图中，我尝试了以下方法：

g <- make_ring(10) + make_full_graph(5)
coords <- layout_(g, as_star())
plot(g, layout = coords)
# try to replicate this example:
coords2 <- add_layout_(g1, coord(g1))

我也尝试过使用this function。这很困难，因为文档中没有示例。

Lay <- layout_igraph_manual(g1, coord(g1))
Lay <- layout_igraph_igraph(g1, coord(g1))

x11()
ggraph(g1, 'igraph', algorithm = 'kk' ) + add_layout_(Lay) +
# layout_igraph_circlepack() + 
geom_edge_link(colour = "black", alpha = 0.8, show.legend = F) + 
geom_node_label(aes(label = NaMe)) + ggtitle("ggraph plot: Cannot allocate    coordinate for each node") + 
ggforce::theme_no_axes()

Answer 1

我不相信作者的意图是直接调用layout_igraph_manual。如果您将布局命名为"manual“，则可以传递手动布局顶点所需的参数。如果我没理解错的话，这给了我你想要的东西：

coords <- coord(g1)
names(coords) <- c("x","y")
coords <- as.data.frame(coords)

ggraph(g1, layout = "manual", circular = FALSE, node.positions = coords)+
  geom_edge_link(colour = "black", alpha = 0.8, show.legend = F) + 
  geom_node_label(aes(label = NaMe)) + ggtitle("ggraph plot: How to allocate coordinate for each node?") + 
  ggforce::theme_no_axes()

根据文档，您的手动布局是一个数据帧，并且包含列x和y，这一点很重要。我已经对您的coord()函数的输出执行了此操作。您可能只想更新它以返回该格式的数据。

Answer 2

使用ggraph时，您通常不必考虑节点坐标-它们是基于所选布局自动提供的。如果您想事先自己计算布局，只需使用手动布局-查看layout_igraph_manual文档

Answer 3

谢谢@ThomasP85 (哇！ggraph的开发人员)。在本例中，我想指定每个节点的坐标。我尝试过layout_igraph_manual、layout_、add_layout_和其他许多工具，但似乎都不起作用。

起作用的是这样的

co2<- data.frame(coord(g1))  # my mistake above, the output of coord() should be a matrix
colnames(co2)<- c("x", "y")
Lay<- createLayout(g1, layout = "nicely") # try any layout
Lay$x<- co2$x  # <== now overwrite their coordinates
Lay$y<- co2$y


x11()  # <==== this is ggraph version of the igraph plot above 
ggraph(graph=g1, data=Lay) + 
geom_edge_link(colour = "black", alpha = 0.5, show.legend = F) + 
geom_node_label(aes(label = NaMe)) + ggtitle("Nodes with higher degree at top, lower degree nodes at the bottom") + 
ggforce::theme_no_axes()

@ThomasP85如果您能提供一个使用layout_igraph_manual的上述代码的工作示例，将不胜感激。